Philip Jones was one of the most powerful men in the country in the days of the two Protectors. He was a member of the Council of State, and on numerous sub-committees: he was on the committee at the end of 1653 to deal with provocative speeches by people like Vavasor Powell (q.v.), and to draft a new ordinance to keep such excesses within the bounds of reason; he was the most prominent member of a commission in 1655 to bring about peace between English merchants and the king of Portugal. To see him coming in with the Treasurer of the Propagation in North Wales soon damped the criticism of the London accountants upon the figures of the latter; and it is next to certainty that it was his word in the Council that saved Botwnnog school from being moved to Pwllheli. Naturally, he did not forget his native town; through his influence Swansea received two charters, one in 1655 one in 1658 — the latter made it into a borough.

Jones had no sympathy whatsoever with extremists and fanatics; this explains his sitting in Cromwell's ‘Other House’ as Philip lord Jones, his doing his utmost to get the Protector to declare himself king, and his being appointed to supervise the Protector's household (it was he who organized the funeral arrangements of Nov. 1658). After Richard Cromwell resigned, Jones became at once the target of attacks from Royalist pamphleteers and the army extremists; and he saw as soon as anybody that the king could not be kept out, and that it would be well to come to terms with the coming powers. There was a dangerous moment in the peevish Convention Parliament (June 1660) when Philip Jones was named as a person who deserved punishment for the part he had played during the Republic, but his friends saw to it that the idea was dropped, helped by some words of diplomatic contrition which he had to sign. In 1661 the Carmarthenshire consistory court brought a charge against him of having (many years before) carried away the organ of S. Mary's Swansea, but it remains a mere record on the books, with no more said about it. In fact, whatever bitter clerics and hostile Royalists might say, Jones had prepared a safe accommodation for himself with the new powers through the kindness and generosity he had shown to some of them when he was in the ascendant (of this there is a good example in his decision of 1656 in favour of Ann, daughter to one of the Carmarthenshire Mansells and niece to the dispossessed principal of Jesus College, Oxford). He retired to the lands he had bought at Fonmon in the Vale of Glamorgan, became high sheriff in 1671, and d. on 5 Sept. 1674. One of the witnesses of his last will was Robert Thomas of Llanfihangel by Cowbridge, M.P. for Cardiff, and one of the five commissioners at Neath in 1655 who declared that the Propagation accounts of Philip Jones and his co-adjutors were correct to the nearest penny. And the name of his youngest son, Oliver, born in 1654, was a living memory of the old friendship with Cromwell and his family.